Detection of gene-environment interactions in a family-based population using SCAD

2017 ◽  
Vol 36 (22) ◽  
pp. 3547-3559 ◽  
Author(s):  
Gwangsu Kim ◽  
Chao-Qiang Lai ◽  
Donna K. Arnett ◽  
Laurence D. Parnell ◽  
Jose M. Ordovas ◽  
...  
Keyword(s):  
Gene Environment ◽  
Family Based

scholarly journals Family-based gene-environment interaction using sequence kernel association test (FGE-SKAT) for complex quantitative traits

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao-Yu Guo ◽  
Reng-Hong Wang ◽  
Hsin-Chou Yang
Keyword(s):  
Complex Traits ◽  
Association Studies ◽  
Association Test ◽  
Whole Genome Sequence ◽  
Environment Interaction ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Sequence Kernel Association Test ◽  
Gene Environment ◽  
Family Based

AbstractAfter the genome-wide association studies (GWAS) era, whole-genome sequencing is highly engaged in identifying the association of complex traits with rare variations. A score-based variance-component test has been proposed to identify common and rare genetic variants associated with complex traits while quickly adjusting for covariates. Such kernel score statistic allows for familial dependencies and adjusts for random confounding effects. However, the etiology of complex traits may involve the effects of genetic and environmental factors and the complex interactions between genes and the environment. Therefore, in this research, a novel method is proposed to detect gene and gene-environment interactions in a complex family-based association study with various correlated structures. We also developed an R function for the Fast Gene-Environment Sequence Kernel Association Test (FGE-SKAT), which is freely available as supplementary material for easy GWAS implementation to unveil such family-based joint effects. Simulation studies confirmed the validity of the new strategy and the superior statistical power. The FGE-SKAT was applied to the whole genome sequence data provided by Genetic Analysis Workshop 18 (GAW18) and discovered concordant and discordant regions compared to the methods without considering gene by environment interactions.

scholarly journals Gene Environment Interactions and Predictors of Colorectal Cancer in Family-Based, Multi-Ethnic Groups

2018 ◽  
Vol 8 (1) ◽  
pp. 10 ◽  
Author(s):  
S. Shiao ◽  
James Grayson ◽  
Chong Yu ◽  
Brandi Wasek ◽  
Teodoro Bottiglieri
Keyword(s):  
Colorectal Cancer ◽  
Ethnic Groups ◽  
Gene Environment ◽  
Family Based

scholarly journals Gene-environment interactions and predictors of breast cancer in family-based multi-ethnic groups

Oncotarget ◽  
2018 ◽  
Vol 9 (49) ◽  
pp. 29019-29035 ◽  
Author(s):  
Mildred C. Gonzales ◽  
James Grayson ◽  
Amanda Lie ◽  
Chong Ho Yu ◽  
Shyang-Yun Pamela K. Shiao
Keyword(s):  
Breast Cancer ◽  
Ethnic Groups ◽  
Gene Environment ◽  
Family Based

scholarly journals Neural Tube Defects and Folate Pathway Genes: Family-Based Association Tests of Gene–Gene and Gene–Environment Interactions

2006 ◽  
Vol 114 (10) ◽  
pp. 1547-1552 ◽  
Author(s):  
Abee L. Boyles ◽  
Ashley V. Billups ◽  
Kristen L. Deak ◽  
Deborah G. Siegel ◽  
Lorraine Mehltretter ◽  
...  
Keyword(s):  
Neural Tube ◽  
Neural Tube Defects ◽  
Association Tests ◽  
Gene Environment ◽  
Folate Pathway ◽  
Family Based

scholarly journals Detection of gene-environment interactions in a family-based population using SCAD

2017 ◽  
Vol 37 (3) ◽  
pp. 506-506
Author(s):  
Gwangsu Kim ◽  
Chao-Qiang Lai ◽  
Donna K. Arnett ◽  
Laurence D. Parnell ◽  
Jose M. Ordovas ◽  
...  
Keyword(s):  
Gene Environment ◽  
Family Based

Testing and Estimating Gene-Environment Interactions in Family-Based Association Studies

Biometrics ◽  
2008 ◽  
Vol 64 (2) ◽  
pp. 458-467 ◽  
Author(s):  
Stijn Vansteelandt ◽  
Dawn L. DeMeo ◽  
Jessica Lasky-Su ◽  
Jordan W. Smoller ◽  
Amy J. Murphy ◽  
...  
Keyword(s):  
Association Studies ◽  
Gene Environment ◽  
Family Based

scholarly journals Testing gene-environment interactions in family-based association studies using trait-based ascertained samples

2013 ◽  
Vol 33 (2) ◽  
pp. 304-318 ◽  
Author(s):  
Weiming Zhang ◽  
Carl D. Langefeld ◽  
Gary K. Grunwald ◽  
Tasha E. Fingerlin
Keyword(s):  
Association Studies ◽  
Gene Environment ◽  
Family Based

scholarly journals Comparison of 2 models for gene–environment interactions: an example of simulated gene–medication interactions on systolic blood pressure in family-based data

2016 ◽  
Vol 10 (S7) ◽  
Author(s):  
Lindsay Fernández-Rhodes ◽  
Chani J. Hodonsky ◽  
Mariaelisa Graff ◽  
Shelly-Ann M. Love ◽  
Annie Green Howard ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Systolic Blood Pressure ◽  
Gene Environment ◽  
Family Based

scholarly journals Using Genome Wide Estimates of Heritability to Examine the Relevance of Gene-Environment Interplay

2016 ◽  
Author(s):  
BENJAMIN W DOMINGUE ◽  
Jason D. Boardman
Keyword(s):  
Genome Wide Association Study ◽  
Environment Interaction ◽  
Education Group ◽  
Gene Environment ◽  
Genome Wide ◽  
Heart Study ◽  
A Genome ◽  
Genome Wide Data ◽  
Higher Educational Attainment ◽  
Family Based

We use genome-wide data from the third generation respondents of the Framingham Heart Study to estimate heritability in body mass index using different quantities of the measured genotype. Heritability decreases rapidly when SNPs implicated by a genome-wide association study are removed but shows essentially no decline when SNPs implicated by a gene-environment interaction in a second genome-wide analysis are removed. This second result is highlighted by our additional finding that the SNPs which explain heritability amongst a subsample defined by higher educational attainment explain no heritability of the heritability in the lower education group, and vice-versa. Finally, we do find consistent heritability estimates when we compare family-based estimates versus those based on measured genotype.

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